DotDG has by far been the most inspiration to me, but other than that, I've basically not used any of the stat blocks from it.
CA, however, has been very helpful for quick plot hooks when I am stuck as well as for things like Orks and the like. I would say that for an average game with no specific enemy, CA is definitely the way to go. If, however, you're doing an investigative/cultist game then DotDG is the way to go (as it is full of all 3 categories of nasties).

As a wargamer, just divide the DH stats by 10, and you will get an 'approximation' of what they'd be on the tabletop version.
Now, as far as stats go, there are some Guardsmen stat blocks on the heresypedia website (Google it). That page also has Chaos Marines and Lords etc (or at least where to find them within the books).
Finally, I should just say, you might want to think more about your campaign. It sounds like you have a bit of an uber-powerful character coming in at the end and solving it for the players. You want the players in the spotlight, not an NPC.
Just my $0.02...

I would love to see horde or mass combat rules (in addition to almost everything listed already... Especially Commissars and Ogryns). Personally, I think you can't have a War book without being able to run a war with it. Am I right?

Excellent! Well, if you have an RPG.net account, then you can probably join in on the main dev thread that it now up there: http://forum.rpg.net/showthread.php?601119-DH-Fan-made-Eldar-Supplement-needs-extra-hands!
Also, email me on psykiekilla@gmail.com and I will send you the working document...
Really excited to be working with you on this!

Greetings all,
A while ago (approximately 800 billion years) I was working on a supplement for Dark Heresy for playing in Eldar campaigns. It was to be called Children of the Stars. Basically, the focus of the book was for people to play as Eldar (and, as this is a massive difference to the normal game, the book was somewhat of a rewrite of the entire system for Chargen etc) but I was intending to include a small section for playing against the Eldar (or having the Eldar as major portions of your game). Essentially, it was an all-round Eldar book.
Anyway, I got side tracked with a few things in life (University, work, etc etc) and I stopped making it. But, I would like to change that...
HOWEVER (and this is where it gets interesting... At least, I hope it does) I believe it would be a lot more possible, and complete, if more than just myself worked on it.
As such, I am looking for people with a variety of skills: (Note, you do not have to have all of these, but you should have at least one so that you can fit into the process... You'll see what I mean)
* A knowledge of the Eldar as a race * A knowledge of the mechanics of Dark Heresy and/or other 40k RPG titles * A knowledge of RPG design basics * Skill with an ink and quill (i.e. able to write well and perhaps come up with some cool short stories to add in) * Skill with a brush (i.e. artists would be helpful as well) * And any other technical skills that would be helpful, such as layouting and the like...
So, is anyone interested?
Thank you and let me know!

Whilst that is a cool mission goal for your players, Adeptus-B is right; the manufactorum would be broken beyond repair (at least under the scope of the PCs). However, you could suggest to the players through the use of an NPC that if the area were to be cleaned up (getting rid of the Chirugeon, and removing the gangers) then perhaps the area would become used again and restored.
In my campaign, I did just that. We had a Sororitas character, and after defeating the Chirugeon the chapel there thought that the daemons were banished by the Sororitas, and proclaimed her a "Living Saint". This caused both a religious outcry, as well as an influx of new people, and the Corscarla was eventually rebuilt after later events of the campaign which lead to this Sororitas being named a Matyr.

I just removed dodging when it comes to bullets all together... I've had no problems thus far. I do, however, give a negative to shooting at someone who ran in their previous turn (thus indicating that they are a difficult target to hit, etc). This is based on Ag bonus (every point higher than BS bonus gives a -10 to enemy shooting).

I've only ever awarded one... When the players thwarted a Chaos-induced rebellion on Ganf Magna by securing a daemon artifact (The Reliquary of the Red Angel) and killing a Bloodhound of Khorne, and the Rogue Psykers responsible for corrupting the peasants. They then, with the civil war stopped, commandeered the local PDF and waged war on a massive horde of Greenskins lead by genetically induced Wyrd-boyz (done so by the Logicians) and killed their Warboss and took down their minor Squiggoth with several RPG rounds thus preventing a far larger Waaagh! from entering the Sector... Only then, did I award them a Fate Point!

Exactly what Zakalwe said... It is an RPG, therefore the GM has COMPLETE CONTROL over what happens, and the skills and talents that are available to the players. I have never understood the mentality of "It says X in the book, therefore that is the case."
Just change it.

Well basically I always saw the Warp as a realm of emotion... Daemons happen to exist because the more active emotions are more prominent, and therefore lash out on the world... Plus, the creation of the Chaos Gods kicked up the waters of the Warp a little...

I can see no problems with this. I have run Edge of Darkness 4 times now with different groups and it is very easy for a single investigative player to get through it. Just either increase his XP as you say or lower the amount of enemies he encounters.

The Warp isn't all maddening, so Warp Entities don't have to be malicious... They are just creatures of emotion. Usually that emotion comes in the form of bad ones, but it is just as easy for weak shadows of people's emotions to remain... Which are basically ghosts.
But if you are having these ghosts being souls or anything like them, then they are Warp Entities...

As has been said, there is little in the canon to tell us, but I would say that most Inquisitors are on a seesaw in this regard. I.e. no one holds that strictly to any one creed... It is far to dangerous to.
Sure, a Puritan is a Puritan, and they will follow their Puritan creed, but such a creed could also say that any even slightly heretical or radical behaviour should be stamped out. Despite this, they aren't going to start shooting Radical Inquisitors left and right. No one is that stupid.
Same thing goes for the Radicals. I am sure every Radical is as suspicious of his fellows as he is of his 'enemies'. The categories are, as has been said, loose stereotypes. It is like saying skin cells, blood cells and brain cells are all cells of the human body, and therefore are the same. It is a ridiculous claim.
Every Inquisitor is unique, and I would be utterly surprised if there was even one who would hold absolutely blindly to any one creed.